[med-svn] [bowtie2] 01/02: Merge tag 'debian/2.3.0-2' into debian/jessie-backports
Andreas Tille
tille at debian.org
Tue Jun 6 13:48:04 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch debian/jessie-backports
in repository bowtie2.
commit 396bcdf8bd8a6b1a219cfcce5e2b8f10dee5cea6
Merge: ffaa174 c3044e3
Author: Andreas Tille <tille at debian.org>
Date: Tue Jun 6 15:30:22 2017 +0200
Merge tag 'debian/2.3.0-2' into debian/jessie-backports
bowtie2 Debian release 2.3.0-2
.gitignore | 26 +
.travis.yml | 20 +
MANUAL | 30 +-
MANUAL.markdown | 36 +-
Makefile | 87 +-
NEWS | 27 +-
README | 8 +
VERSION | 2 +-
aligner_result.cpp | 2 +-
aligner_result.h | 2 +-
aligner_seed.cpp | 18 +-
aligner_seed2.cpp | 19 +-
aligner_seed2.h | 2 -
aligner_sw_common.h | 13 +-
aligner_swsse_ee_i16.cpp | 1 -
aligner_swsse_ee_u8.cpp | 1 -
aligner_swsse_loc_u8.cpp | 1 -
aln_sink.h | 8 -
alphabet.cpp | 199 -
alphabet.h | 72 -
blockwise_sa.h | 21 +-
bt2_build.cpp | 14 +-
bt2_inspect.cpp | 6 +-
bt2_search.cpp | 211 +-
bt2_search.h | 4 +-
cpu_numa_info.cpp | 9 +
cpu_numa_info.h | 6 +
debian/changelog | 74 +
debian/compat | 2 +-
debian/control | 12 +-
debian/copyright | 5 +-
debian/help2man-wrapper | 5 +-
debian/patches/do-not-rebuild-during-test.patch | 56 +
debian/patches/hardening.patch | 136 +-
debian/patches/indentation.patch | 17 +
debian/patches/reproducible.patch | 156 +
debian/patches/series | 5 +
debian/patches/single-cpu-for-test.patch | 51 +
...st_requiring_non-free_libmath-random-perl.patch | 198 +
debian/rules | 33 +-
debian/upstream/edam | 56 +
debian/upstream/metadata | 3 +
debian/watch | 5 +-
diff_sample.h | 4 +-
doc/images/bowtie_logo.png | Bin 0 -> 16419 bytes
doc/images/osi-certified.gif | Bin 0 -> 2712 bytes
doc/images/sflogo.png | Bin 0 -> 1177 bytes
doc/images/university.small.horizontal.white.png | Bin 0 -> 35224 bytes
doc/manual.html | 1429 +++---
doc/release.txt | 153 +
doc/website/faq.shtml | 34 +
doc/website/faq.ssi | 68 +
doc/website/foot.ssi | 12 +
doc/website/index.html | 9 +
doc/website/index.shtml | 60 +
doc/website/manual.shtml | 33 +
doc/{manual.html => website/manual.ssi} | 56 +-
doc/website/news.shtml | 35 +
doc/website/old_news.ssi | 359 ++
doc/website/other_tools.shtml | 33 +
doc/website/push.sh | 17 +
doc/website/push_images.sh | 16 +
doc/website/recent_news.ssi | 104 +
doc/website/rhsidebar.ssi | 196 +
doc/website/top.ssi | 16 +
dp_framer.cpp | 3 +-
dp_framer.h | 3 +-
filebuf.h | 1 +
opts.h | 2 +-
pat.cpp | 2030 ++++----
pat.h | 1852 +++----
pthreadGC2.dll | Bin 0 -> 60273 bytes
read.h | 102 +-
read_qseq.cpp | 383 +-
ref_read.cpp | 34 +-
sam.cpp | 120 +-
sam.h | 8 -
scoring.cpp | 1 -
scoring.h | 2 +-
scripts/sa.py | 79 +
scripts/sim/AlignmentCheck.pm | 859 ++++
scripts/sim/DNA.pm | 287 ++
scripts/sim/Mutate.pm | 301 ++
scripts/sim/RandDNA.pm | 191 +
scripts/sim/SampleRead.pm | 244 +
scripts/sim/Sim.pm | 1040 ++++
scripts/sim/Test.pm | 47 +
scripts/sim/contrib/ForkManager.pm | 412 ++
scripts/sim/run.pl | 133 +
scripts/sim/run.sh | 37 +
scripts/sim/unit.sh | 23 +
scripts/test/.gitignore | 1 +
scripts/test/DNA.pm | 127 +
scripts/test/README.md | 44 +
scripts/test/benchmark/benchmarks.py | 275 ++
scripts/test/benchmark/data/conf/acc.json | 44 +
scripts/test/benchmark/data/conf/seta.bench | 59 +
scripts/test/benchmark/data/conf/speed.json | 44 +
scripts/test/benchmark/run.py | 128 +
scripts/test/benchmark/samreader.py | 128 +
scripts/test/big_data/reads/human_reads.fa | 8 +
scripts/test/big_data/reads/mouse_reads.fa | 8 +
scripts/test/bt2face.py | 39 +
scripts/test/btdata.py | 199 +
scripts/test/dataface.py | 81 +
scripts/test/large_idx.py | 110 +
scripts/test/regressions.py | 207 +
scripts/test/simple_tests.pl | 5070 ++++++++++++++++++++
scripts/test/simple_tests.sh | 34 +
search_globals.h | 5 -
simple_func.h | 4 +
sstring.cpp | 4 +-
sstring.h | 142 +-
threading.h | 46 +-
114 files changed, 15272 insertions(+), 4022 deletions(-)
diff --cc debian/changelog
index 349d8e4,7e8c5a2..556ab8b
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,77 +1,83 @@@
+ bowtie2 (2.3.0-2) unstable; urgency=medium
+
+ * Team upload.
+
+ [ Sascha Steinbiss ]
+ * Skip tests involving simulated reads to avoid use of non-free build-dep
+ libmath-random-perl again.
+ Closes: #852546
+ * Add libclone-perl build dependency.
+
+ [ Alexandre Mestiashvili ]
+ * Add patch suppressing -Wmisleading-indentation warnings.
+
+ [ Steffen Moeller ]
+ * Adjust EDAM annotations.
+
+ -- Sascha Steinbiss <satta at debian.org> Wed, 25 Jan 2017 16:27:13 +0100
+
+ bowtie2 (2.3.0-1) unstable; urgency=medium
+
+ * Team upload.
+
+ [ Andreas Tille ]
+ * New upstream version
+ * Code available on Github
+ * debhelper 10
+ * Remove Carlos Borroto from Uploaders
+ * Remove code from test suite that is requiring non-free package
+ libmath-random-perl
+ * New Build-Depends to run build time test: liblocal-lib-perl
+
+ [ Sascha Steinbiss ]
+ * Even more new Build-Depends: libmath-random-perl, libtest-deep-perl
+ * Disable rebuilding during tests
+
+ -- Sascha Steinbiss <satta at debian.org> Sat, 14 Jan 2017 07:50:51 +0000
+
+ bowtie2 (2.2.9-4) unstable; urgency=medium
+
+ * Team upload.
+ * Make build reproducible by adding compiler flags
+ setting -fdebug-prefix-map.
+
+ -- Sascha Steinbiss <satta at debian.org> Thu, 25 Aug 2016 12:47:33 +0000
+
+ bowtie2 (2.2.9-3) unstable; urgency=medium
+
+ * Team upload.
+ * Fix building with GCC 6.
+ Closes: #831157.
+
+ -- Sascha Steinbiss <satta at debian.org> Sat, 16 Jul 2016 03:22:51 +0000
+
+ bowtie2 (2.2.9-2) unstable; urgency=medium
+
+ * Team upload.
+ * Make build reproducible.
+ - Remove embedding of build hostname, time and compiler.
+ - Fix help2man wrapper heredoc.
+ - Sort wildcard expansions in Makefile.
+ - Pin down language settings.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 21 May 2016 17:18:25 +0000
+
+ bowtie2 (2.2.9-1) unstable; urgency=medium
+
+ * Imported Upstream version 2.2.9
+ * Bump Standards-Version
+ * Revert the commit with applied patch
+ * Update hardening.patch
+ * Cleanup d/rules, remove CPPFLAGS as they are imported anyway
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de> Thu, 28 Apr 2016 09:26:48 +0200
+
+bowtie2 (2.2.8-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Andreas Tille <tille at debian.org> Tue, 22 Mar 2016 09:30:26 +0100
+
bowtie2 (2.2.8-1) unstable; urgency=medium
[ Andreas Tille ]
--
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